Mercurial > repos > ebi-gxa > scanpy_run_tsne
diff scanpy-run-tsne.xml @ 16:9d2b6c6f9e07 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit c02d457c74016980672e64832e6cad31d703edcd-dirty"
| author | ebi-gxa |
|---|---|
| date | Tue, 29 Sep 2020 14:10:52 +0000 |
| parents | b5e1939cc155 |
| children | 2c6340dad187 |
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--- a/scanpy-run-tsne.xml Thu Sep 17 16:28:31 2020 +0000 +++ b/scanpy-run-tsne.xml Tue Sep 29 14:10:52 2020 +0000 @@ -1,12 +1,11 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>visualise cell clusters using tSNE</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ -#from pathlib import Path #set embeddings_tsv='embeddings.tsv' ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-run-tsne @@ -18,7 +17,9 @@ #end if #if $settings.default == "false" #if $settings.perplexity_file - #set perplexity = Path($settings.perplexity_file.__str__).read_text().strip() + #set f = open($settings.perplexity_file.__str__) + #set perplexity = f.read().strip() + #silent f.close #elif $settings.perplexity #set perplexity = $settings.perplexity.__str__.strip() #end if @@ -100,6 +101,22 @@ <param name="input_format" value="anndata"/> <param name="output_format" value="anndata"/> <param name="default" value="false"/> + <param name="perplexity_file" value="perplexity.txt"/> + <param name="embeddings" value="true"/> + <param name="random_seed" value="0"/> + <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/> + <output name="output_embed" file="run_tsne.embeddings.tsv" ftype="tabular" compare="sim_size"> + <assert_contents> + <has_n_columns n="3"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_obj_file" value="find_cluster.h5"/> + <param name="input_format" value="anndata"/> + <param name="output_format" value="anndata"/> + <param name="default" value="false"/> + <param name="perplexity" value="30"/> <param name="embeddings" value="true"/> <param name="random_seed" value="0"/> <output name="output_h5" file="run_tsne.h5" ftype="h5" compare="sim_size"/>